Opening Matlab 2013b throws lot of warnings and java errors

I am seeing lots of warnings and java errors while opening Matlab 2013b,

Warning: Function license has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict.
Warning: Function version has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict.
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\rtw\coder_foundation\tfl
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\rtw\targets\c166\c166
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\rtw\targets\c166\c166demos
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\rtw\targets\mpc555dk
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\rtw\targets\mpc555dk\common\configuration
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\rtw\targets\mpc555dk\mpc555demos
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\rtw\targets\mpc555dk\mpc555dk
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\rtw\targets\mpc555dk\pil
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\rtw\targets\mpc555dk\rt\blockset
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\rtw\targets\mpc555dk\rt\blockset\mfiles
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\rtw\targets\tasking\tasking
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\rtw\targets\tasking\taskingdemos
Warning: Name is nonexistent or not a directory: D:\matlab2013\help\toolbox\vision\examples
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\daq\daqblks\daqblks
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\daq\daqblks\daqmasks
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\daq\daqblks\daqmex
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\embeddedcoder
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\idelink\extensions\adivdsp\mdlinfo
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\idelink\extensions\adivdsp\rtw
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\idelink\extensions\adivdsp\tfl
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\idelink\extensions\adivdsp\vdspblks
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\idelink\extensions\adivdsp\vdspdemos
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\idelink\extensions\ghsmulti
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\idelink\extensions\ghsmulti\mdlinfo
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\idelink\extensions\ghsmulti\multiblks
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\idelink\extensions\ghsmulti\multidemos
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\idelink\extensions\ghsmulti\rtw
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\idelink\extensions\ghsmulti\tfl
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\idelink\extensions\wrworkbench
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\idelink\extensions\wrworkbench\mdlinfo
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\idelink\extensions\wrworkbench\registry
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\idelink\extensions\wrworkbench\wrworkbenchblks
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\idelink\foundation\lfsocket\lfsocket
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\idelink\foundation\pjtgenerator\blks\utils
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\idelink\foundation\pjtgenerator\hookpoints
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\instrument\instrument
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\instrument\instrumentblks\instrumentblks
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\instrument\instrumentblks\instrumentmasks
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\instrument\instrumentblks\instrumentmex
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\instrument\instrumentdemos
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\physmod\data_manager\data_manager
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\physmod\foundation\foundation
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\physmod\gl\core\m
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\physmod\gl\sli\m
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\physmod\logging\base\m
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\physmod\logging\mli\m
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\physmod\pmir\pmir
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\physmod\simscape_language\simscape_language
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\physmod\simulation\base\m
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\physmod\unit_manager\unit_manager
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\rf\openif
Warning: Name is nonexistent or not a directory: D:\matlab2013\toolbox\sam\m3i
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\shared\eml\eml 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\shared\statslib 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\simrf\simrfdemos 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\simrf\simrfmasks 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\slvnv\do178b 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\slvnv\iec61508 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\slvnv\rmidemos 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\slvnv\simcovdemos 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\slvnv\slvnvdemos 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\slvnv\styleguide 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\stats\classreg 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\stats\stats 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\stats\statsdemos 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\symbolic\symbolic 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\symbolic\symbolicdemos 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\target\extensions\operatingsystem\vxworks\blks 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\target\extensions\operatingsystem\vxworks\blks\masks 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\target\extensions\operatingsystem\vxworks\blks\mex 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\target\extensions\operatingsystem\vxworks\src 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\target\extensions\processor\blackfin 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\target\extensions\processor\blackfin\blackfindemos 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\target\extensions\processor\blackfin\blks 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\target\extensions\processor\blackfin\blks\masks 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\target\extensions\processor\blackfin\blks\mex 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\target\extensions\processor\tic2000\blks\masks 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\target\extensions\processor\tic2000\tic2000demos 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\vision\vision 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\vision\visiondemos 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\vision\visionutilities 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\vision\visionutilities\visioninit 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\vision\visionutilities\visionmex 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\wavelet\compression 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\wavelet\wavedemo 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\wavelet\wavelet 
Warning: Name is nonexistent or not a directory:
D:\matlab2013\toolbox\wavelet\wmultisig1d 
Warning: Name is nonexistent or not a directory:
D:\lpaa-smartamp\rdgui\cfg\tas2555 
Warning: Name is nonexistent or not a directory:
D:\lpaa-smartamp\rdgui\cfg\tas2557 
Warning: Name is nonexistent or not a directory:
D:\lpaa-smartamp\rdgui\cfg\tas2557_revB2\outputControls 
ERROR: Error starting reference:file:/D:/matlab2013/java/jar/cmlink/implementations/svnintegration.jar (org.osgi.framework.BundleException: Activator start error in bundle com.mathworks.cmlink [8].)
java.lang.NoClassDefFoundError: com/mathworks/toolbox/shared/computils/reflection/Caller
	at com.mathworks.cmlink.util.adapter.wrappers.CMAdapterFactoryWrapper.<init>(CMAdapterFactoryWrapper.java:16)
	at com.mathworks.cmlink.implementations.svnintegration.CmdLineSVNAdapterFactory.<init>(CmdLineSVNAdapterFactory.java:10)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
	at java.lang.reflect.Constructor.newInstance(Unknown Source)
	at java.lang.Class.newInstance0(Unknown Source)
	at java.lang.Class.newInstance(Unknown Source)
	at com.mathworks.util.osgi.ServicesActivator.registerServicePair(ServicesActivator.java:58)
	at com.mathworks.util.osgi.ServicesActivator.parseServices(ServicesActivator.java:38)
	at com.mathworks.util.osgi.ServicesActivator.start(ServicesActivator.java:33)
	at org.apache.felix.framework.util.SecureAction.startActivator(SecureAction.java:589)
	at org.apache.felix.framework.Felix.startBundle(Felix.java:1458)
	at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:984)
	at org.apache.felix.framework.StartLevelImpl.run(StartLevelImpl.java:263)
	at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.ClassNotFoundException: com.mathworks.toolbox.shared.computils.reflection.Caller
	at java.net.URLClassLoader$1.run(Unknown Source)
	at java.net.URLClassLoader$1.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(Unknown Source)
	at java.lang.ClassLoader.loadClass(Unknown Source)
	at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
	at java.lang.ClassLoader.loadClass(Unknown Source)
	... 16 more
Exception in thread "ContributedToolsLoader" java.lang.NoClassDefFoundError: com/mathworks/appmanagement/AppManagementApiBuilder
	at com.mathworks.mde.desk.ContributedTools.<init>(ContributedTools.java:104)
	at com.mathworks.mde.desk.ContributedToolsLoader$1.run(ContributedToolsLoader.java:18)
	at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.ClassNotFoundException: com.mathworks.appmanagement.AppManagementApiBuilder
	at java.net.URLClassLoader$1.run(Unknown Source)
	at java.net.URLClassLoader$1.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(Unknown Source)
	at java.lang.ClassLoader.loadClass(Unknown Source)
	at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
	at java.lang.ClassLoader.loadClass(Unknown Source)
	... 3 more
Exception in thread "Startup Class Loader" java.lang.NoClassDefFoundError: com/jniwrapper/PlatformContext
	at com.teamdev.jxbrowser.mozilla.MozillaBrowserType.isSupported(Unknown Source)
	at com.mathworks.html.jxbrowser.JxBrowserSettings.getBrowserTypeValues(JxBrowserSettings.java:46)
	at com.mathworks.html.jxbrowser.JxBrowserSettings.buildSupportedProperties(JxBrowserSettings.java:33)
	at com.mathworks.html.jxbrowser.JxBrowserSettings.<clinit>(JxBrowserSettings.java:23)
	at com.mathworks.html.BrowserSettings.getAllSettingsInstances(BrowserSettings.java:59)
	at com.mathworks.html.BrowserSettings.<clinit>(BrowserSettings.java:22)
	at com.mathworks.mlwidgets.html.HtmlComponentFactory.<clinit>(HtmlComponentFactory.java:54)
	at java.lang.Class.forName0(Native Method)
	at java.lang.Class.forName(Unknown Source)
	at com.mathworks.mde.desk.StartupClassLoader$LoadInfo.<init>(StartupClassLoader.java:80)
	at com.mathworks.mde.desk.StartupClassLoader.createLoadInfos(StartupClassLoader.java:161)
	at com.mathworks.mde.desk.StartupClassLoader.access$400(StartupClassLoader.java:25)
	at com.mathworks.mde.desk.StartupClassLoader$2.run(StartupClassLoader.java:178)
	at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.ClassNotFoundException: com.jniwrapper.PlatformContext
	at java.net.URLClassLoader$1.run(Unknown Source)
	at java.net.URLClassLoader$1.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(Unknown Source)
	at java.lang.ClassLoader.loadClass(Unknown Source)
	at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
	at java.lang.ClassLoader.loadClass(Unknown Source)
	... 14 more

Interestingly, I get Java errors (below) if I click Preferences button too, then Preferences panel opens but the window is empty and doesn't show any options.

Exception in thread "AWT-EventQueue-0" java.lang.IllegalArgumentException: com.mathworks.appmanagement.AppsPreferencePanel no class matches the supplied argument
	at com.mathworks.mlwidgets.prefs.PrefsDialog.getPrefsEditorPanelFactory(PrefsDialog.java:397)
	at com.mathworks.mlwidgets.prefs.PrefsDialog.registerPanel(PrefsDialog.java:358)
	at com.mathworks.mlwidgets.prefs.PrefsDialogRegistrar.preRegisterPanels(PrefsDialogRegistrar.java:47)
	at com.mathworks.mlwidgets.prefs.PrefsDialog.initialize(PrefsDialog.java:101)
	at com.mathworks.mlwidgets.prefs.PrefsDialog.access$500(PrefsDialog.java:32)
	at com.mathworks.mlwidgets.prefs.PrefsDialog$4.run(PrefsDialog.java:277)
	at com.mathworks.mlwidgets.prefs.PrefsDialog.showPrefsDialog(PrefsDialog.java:291)
	at com.mathworks.mlwidgets.prefs.PrefsDialog.doShowPrefsDialog(PrefsDialog.java:251)
	at com.mathworks.mlwidgets.prefs.PrefsDialog.showPrefsDialog(PrefsDialog.java:127)
	at com.mathworks.mlwidgets.prefs.PrefsDialog.showLastPrefsDialog(PrefsDialog.java:164)
	at com.mathworks.mlservices.MLPrefsDialogServices.showLastPrefsDialog(MLPrefsDialogServices.java:45)
	at com.mathworks.mde.desk.MLDesktop$PreferencesAction.actionPerformed(MLDesktop.java:2651)
	at com.mathworks.mwswing.ChildAction.actionPerformed(ChildAction.java:214)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at com.mathworks.toolstrip.plaf.RegularButtonUI$RegularToolstripButtonListener.mouseReleasedImpl(RegularButtonUI.java:327)
	at com.mathworks.toolstrip.plaf.RegularButtonUI$RegularToolstripButtonListener.mouseReleased(RegularButtonUI.java:321)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at com.mathworks.mwswing.MJButton.processMouseEvent(MJButton.java:348)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$200(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)

Any help is appreciated.

[Walter Roberson]

start with

restoredefaultpath

rehash toolboxcache

savepath

[Selvaraj Karuppusamy]

Thanks, I tried running the commands in command window, but it didn't make any difference.

Matlab 2012b, 2015b also installed in the PC. I will remove these installations and try again.

Answer 1

[Selvaraj Karuppusamy]

I have figured out the issue. As I mentioned earlier, 2011b also was installed in the PC.

For some reason, an environment variable called 'Matlabpath' had the value as

'C:\Program Files (x86)\MATLAB\R2011b\toolbox\local;C:\Program Files (x86)\MATLAB\R2011b\toolbox;'

After removing the Matlabpath environment variable, the warnings and java errors disappeared. And Preferences panel started working too.

I think Matlab 2011b also should work without any issues since 2011b location is already available in the 'Path' environement variable. I will update the answer if I face any issues.